[gmx-users] extracting water molecules from trajectory

[T.A.Wassenaar at chem.rug.nl]

Hi Kay,

Actually, I've got a modified versions of src/gmxlib/pbc.c and
src/tools/trjconv.c which do just that; adding the distance from one group
to the other to the b-factor field. I can mail you the sources a bit later
(that is, when I'm on the lab again and I haven't forgotten). In case it
slips my mind :S send me a reminder...

Cheers,

Tsjerk


 On Wed, 19 May 2004, Kay Gottschalk wrote:

> thanks, works:) Would be neat to have the protein-water distance as  
> b-factor in the output-pdb - where would I have to change things to get  
> that done?
> Cheers,
> K.
> 
> On May 19, 2004, at 5:15 PM, David van der Spoel wrote:
> 
> > On Wed, 2004-05-19 at 15:58, Kay Gottschalk wrote:
> >> Hi all,
> >>
> >> I recently read something in the discussion list about extracting  
> >> water
> >> from a trajectory that is in a certain distance to the protein.
> >> Unfortunately I can't find it anymore. Could you please update me on
> >> how to do that?
> > trjorder
> >> Thanks,
> >> K.
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> > --  
> > David.
> > _______________________________________________________________________ 
> > _
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone:  +46 18 471 4205  fax: +46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org    
> > http://xray.bmc.uu.se/~spoel
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> > +
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~